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Bryan Krause
Bryan Krause
12:36 AM
@canadianer Haha that is odd, especially when I was your upvote :-P
 
 
2 hours later…
theforestecologist
theforestecologist
2:18 AM
I'm going away for a little bit. Trying to wrap up my PhD.
Whatever you all do, don't let canadianer convince you to get rid of species ID questions ;p.
I'll see you all on the other side!!!
 
Just win baby
Just win baby
See you :-)
Good luck!
 
 
2 hours later…
canadianer
canadianer
4:24 AM
@theforestecologist Ah, this is the perfect opportunity...
Good luck with your studies
@BryanKrause I must be making enemies ;)
 
another 'Homo sapien'
another 'Homo sapien'
4:46 AM
@canadianer so when are we starting (don't tell @theforestecologist that I'm also with you :P)?
 
Just win baby
Just win baby
:O
How did you do that?
 
another 'Homo sapien'
another 'Homo sapien'
@Justwinbaby do what? You're asking me, right?
 
Just win baby
Just win baby
Yes. That image was not there a minute ago.
 
another 'Homo sapien'
another 'Homo sapien'
Image?
I didn't do anything...related to image :P
 
Just win baby
Just win baby
3 hours ago, by theforestecologist
user image
That^ just popped up out of nowhere :-/
 
another 'Homo sapien'
another 'Homo sapien'
4:51 AM
Dude that's not me
Maybe it was taking time to load on your phone (or computer or whatever device)
 
Just win baby
Just win baby
VERY strange, that has never happened before.
 
another 'Homo sapien'
another 'Homo sapien'
AFAIK images on chat load after everything else has already loaded (scripts of page)
 
Just win baby
Just win baby
Right, that's gotta be it.
But 3 hours? Later.
 
another 'Homo sapien'
another 'Homo sapien'
¯\_(ツ)_/¯
Server was down probably...
 
Just win baby
Just win baby
Yeah, the router has been acting up again.
 
another 'Homo sapien'
another 'Homo sapien'
4:57 AM
Oh I know about computers (^o^)丿
 
Just win baby
Just win baby
dang new fangled contraptions :-)
 
canadianer
canadianer
@another'Homosapien' right now... shhhhh...
 
another 'Homo sapien'
another 'Homo sapien'
@canadianer (ㆁωㆁ*)
 
 
2 hours later…
another 'Homo sapien'
another 'Homo sapien'
6:34 AM
Indeed a nice effort!
 
 
3 hours later…
WYSIWYG
WYSIWYG
10:02 AM
@terdon Yeah I shall.
 
WYSIWYG
WYSIWYG
10:38 AM
0
Q: How to read FCS files using open source libraries?

WYSIWYGFCS is a patented data format used for storing flow cytometry data. The most recent version is FCS3.1. There is some documentation on the format but there is no information on how to read these files. There are some R packages and a MATLAB code to read FCS file but I am looking for standard libra...

file-formats
 
terdon
terdon
@WYSIWYG Cool. By the way, please don't ask questions as "How to foo?", "how to" is a declaration, not a question. So "how to foo" is fine for the title of a post explaining how to foo but wrong for a question asking how to foo. It's weird, I know.
 
WYSIWYG
WYSIWYG
@terdon Okay.. I'll edit it.
 
terdon
terdon
Already done.
And sorry, I know that's a ridiculously minor point, it's just one of my pet peeves.
 
WYSIWYG
WYSIWYG
@terdon you became a mod at bioinformatics too :P
 
terdon
terdon
Yes, pro-tem :)
Finally I'm a mod on a site on whose subject matter I can honestly claim actual expertise in! Whohoo! :P
 
Secret
Secret
11:09 AM
> In 2013, Sorcha Mc Ginty, a biologist then at the University of Zurich, and her colleagues created a computer model showing that plasmids — genes that move from one bacterium to another — help spur the evolution of cooperation within bacterial communities.
In 2015, a group at Paris Descartes University experimentally demonstrated that when bacteria exchange certain plasmids, the plasmids reprogram the recipient bacteria with genetic information that compels them to contribute to the common good.
WTF?
is it selfish gene all over again?
 
WYSIWYG
WYSIWYG
@terdon Regarding your question on reading fastq.gz files.
2
Q: Fast way to count number of reads and number of bases in a fastq file?

terdonI am looking for a tool, preferably written in C or C++, that can quickly and efficiently count the number of reads and the number of bases in a compressed fastq file. I am currently doing this using zgrep and awk: zgrep . foo.fasq.gz | awk 'NR%4==2{c++; l+=length($0)} END{ ...

ngs fastq software-recommendation benchmarking
It would be nice if SRA or any NGS machine that generates a gzip compressed fastq, writes optional metadata.
Of course you can't add everything i.e. base composition etc (as asked in the other question) but adding read counts should be pretty doable.
However, I don't know how to read/write gzip metadata. Trying hard to figure it out but not getting the right resource.
 
Secret
Secret
> Another question raised in the Nature Communications paper is whether the presence of altruism-promoting microbes could kick off an evolutionary arms race between microbes and their hosts. It might be in the hosts’ best interest, after all, to resist being manipulated by the microbes:
Such resistance would mean hosts could keep more resources for themselves, increasing their odds of survival. “If the host has a mutation that makes it resistant to the manipulation of the microbe, the host could start behaving less altruistically,” Hadany said.
> Yet microbes could respond, she added, by finding new ways to manipulate hosts — or even by striking a win-win deal with them: “A new microbe could evolve, this microbe could spread in the population, and while the microbe benefits, the host also benefits.” But regardless of which one benefits more, microbes usually have an edge on their hosts in one major area, she said: “There are many more microbe generations, [so] the microbes have an evolutionary advantage.”
This is why ecology is interesting, it makes you think about interactions between groups in ways you don't normal think of
> “Each unitary organism is associated with bacteria, viruses and so on,” he said. “You can’t look at the altruism without looking at the host.” Hadany said her research has transformed her conception of free will. “Any behavior — I’m now thinking, ‘Is it me, or is it my microbes?’”
 
terdon
terdon
11:35 AM
@WYSIWYG It would, but I need this to deal with fastq files generated by clients. I have no control over the generation process so I need to be able to do it myself.
 

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